Danaher_plot output

This is an result for the gene singatures as well as assigned cell type for each cluster based on Danaher et al.

knitr::opts_chunk$set(cache=TRUE)


sig_plot <- visualize_clusters(cluster_tsne$cell_type,cluster_tsne[c("TSNE.1","TSNE.2")],title="Danaher cell-type labels",legend_anno= sort(unique(cluster_tsne[,"name_type"])))+scale_color_manual(values = colorRampPalette(c("blue", "red","yellow"))( length(sort(unique(cluster_tsne[,"name_type"])))))+  annotate("text", x = tsne_center[, 1], y = tsne_center[, 2], size = 5,label=c(1:length(tsne_center[,1])))

sig_plot

top_sig <- data.frame(t(sapply(unique(all_type_expr_table$Cluster),function(x){ all_type_expr_table[all_type_expr_table$Cluster == x,][which(all_type_expr_table$precent_count[all_type_expr_table$Cluster == x] == max(all_type_expr_table$precent_count[all_type_expr_table$Cluster == x])),] })))
top_sig$Signature <-lapply(top_sig$Signature,function(y){paste(y)})
top_sig$Cluster <-unique(unlist(top_sig$Cluster))
top_sig <- merge(y=top_sig, x=cluster_type[,c("Cluster","name_type")],by="Cluster")
colnames(top_sig)[2] <- "Assigned_Type"
kable(top_sig)

Cluster	Assigned_Type	Signature	Barcode_count	total_all_gene_Exp	avg_non_zero	SD	cell_total_count	precent_count	cell_mean_expression	cell_mean_expression_sum	cell_mean_expression_sd
1	CD45	Macrophages	832	5571	5.435	3.699	963	86.397	0.634	611	24.751
2	T_cells	T_cells	11147	103645	4.073	3.46	11716	95.143	0.658	7705	85.623
3	T_cells	T_cells	16150	139048	3.921	3.382	17068	94.622	0.602	10272.333	93.576
4	CD45	Neutrophils	546	1239	1.998	2.304	1768	30.882	0.06	106.286	5.159
5	Macrophages	Macrophages	34	177	5.206	3.208	75	45.333	0.223	16.75	3.172
6	B_cells	B_cells	2187	21816	4.088	3.624	2282	95.837	0.507	1157.889	29.179
7	Cytotoxic_cells	Cytotoxic_cells	5882	283649	7.919	5.925	5900	99.695	3.563	21021.4	295.397
8	Cytotoxic_cells	Cytotoxic_cells	183	1727	7.256	4.298	202	90.594	0.521	105.3	10.058
9	Macrophages	Macrophages	10	16	1.6	1.897	25	40	0.11	2.75	0.901
10	Mast_cells	Macrophages, Mast_cells	1, 1	1, 9	1, 3	NA, 3.464	1, 1	100, 100	0.25, 1	0.25, 1	0.25, 1

cat("\n")

counter <-1
colnames(score_by_cluster) <- names(cell_list)
apply(score_by_cluster, 1,function(x) { plot_x <- plot(x,ylab="mean expression level per cell",xlab="cell type", main=c("Cluster",counter))
plot_x <- text(x, names(cell_list), cex=0.6, pos=4, col="red")
sum_table <- kable(all_type_expr_table[all_type_expr_table$Cluster == counter,])
plot_x
cat("\n")
print(sum_table)
cat("\n")

counter <<- counter + 1})

	Cluster	Signature	Barcode_count	total_all_gene_Exp	avg_non_zero	SD	cell_total_count	precent_count	cell_mean_expression	cell_mean_expression_sum	cell_mean_expression_sd
3	1	B_cells	28	55	1.528	2.360	963	2.908	0.005	5	1.56
4	1	CD45	480	1681	3.502	3.304	963	49.844	0.811	781	42.485
5	1	CD8_T_cells	39	114	2.651	2.869	963	4.050	0.031	29.5	5.545
6	1	Cytotoxic_cells	303	1376	3.193	4.026	963	31.464	0.101	97.5	14.523
7	1	Exhausted_CD8	161	284	1.690	1.945	963	16.719	0.049	47.25	3.961
8	1	Macrophages	832	5571	5.435	3.699	963	86.397	0.634	611	24.751
9	1	Neutrophils	311	654	1.827	2.113	963	32.295	0.061	59.143	3.703
10	1	NK_CD56dim_cells	21	21	1.000	0.000	963	2.181	0.005	5.25	1.146
11	1	NK_cells	6	25	3.571	3.207	963	0.623	0.003	3.333	1.491
12	1	T_cells	143	638	2.913	2.992	963	14.849	0.054	52.167	5.403
13	1	Th1_cells	9	15	1.667	2.000	963	0.935	0.01	10	3.464
14	1	Treg	2	2	1.000	0.000	963	0.208	0.002	2	1.414

	Cluster	Signature	Barcode_count	total_all_gene_Exp	avg_non_zero	SD	cell_total_count	precent_count	cell_mean_expression	cell_mean_expression_sum	cell_mean_expression_sd
15	2	B_cells	340	795	2.049	2.444	11716	2.902	0.005	56.222	4.366
16	2	CD45	3646	9692	2.658	2.807	11716	31.120	0.42	4922	91.324
17	2	CD8_T_cells	2649	11130	3.312	3.172	11716	22.610	0.222	2597.5	60.235
18	2	Cytotoxic_cells	7866	112444	5.236	4.344	11716	67.139	0.529	6196.1	104.86
19	2	DC	42	60	1.429	1.564	11716	0.358	0.001	15	2.38
20	2	Exhausted_CD8	1778	3240	1.724	1.991	11716	15.176	0.046	533.75	13.709
21	2	Macrophages	282	408	1.442	1.613	11716	2.407	0.007	77	4.835
22	2	Mast_cells	3	10	3.333	4.041	11716	0.026	0	1.25	0.829
23	2	Neutrophils	19	25	1.316	1.376	11716	0.162	0	2.857	0.67
24	2	NK_CD56dim_cells	173	268	1.540	1.779	11716	1.477	0.004	48.25	3.929
25	2	NK_cells	402	1033	2.275	2.524	11716	3.431	0.016	189.333	10.934
26	2	T_cells	11147	103645	4.073	3.460	11716	95.143	0.658	7705	85.623
27	2	Th1_cells	305	408	1.338	1.393	11716	2.603	0.028	323	19
28	2	Treg	84	163	1.940	2.214	11716	0.717	0.008	98	11.314

	Cluster	Signature	Barcode_count	total_all_gene_Exp	avg_non_zero	SD	cell_total_count	precent_count	cell_mean_expression	cell_mean_expression_sum	cell_mean_expression_sd
29	3	B_cells	207	449	1.919	2.297	17068	1.213	0.002	32.444	2.927
30	3	CD45	4863	11961	2.460	2.661	17068	28.492	0.368	6286	99.499
31	3	CD8_T_cells	4141	21377	3.927	3.352	17068	24.262	0.274	4681	85.15
32	3	Cytotoxic_cells	5187	13357	2.174	2.567	17068	30.390	0.046	791.2	15.642
33	3	DC	8	8	1.000	0.000	17068	0.047	0	2.667	0.943
34	3	Exhausted_CD8	1001	1495	1.477	1.644	17068	5.865	0.016	275	9.083
35	3	Macrophages	248	321	1.294	1.309	17068	1.453	0.004	65.25	4.25
36	3	Mast_cells	4	16	4.000	3.464	17068	0.023	0	1.5	0.791
37	3	Neutrophils	31	38	1.188	1.061	17068	0.182	0	4.714	0.869
38	3	NK_CD56dim_cells	137	173	1.263	1.232	17068	0.803	0.002	35.75	3.112
39	3	NK_cells	28	51	1.594	1.881	17068	0.164	0.001	12	2.494
40	3	T_cells	16150	139048	3.921	3.382	17068	94.622	0.602	10272.333	93.576
41	3	Th1_cells	64	82	1.281	1.278	17068	0.375	0.004	67	8.544
42	3	Treg	30	55	1.833	2.167	17068	0.176	0.002	35	6.856

	Cluster	Signature	Barcode_count	total_all_gene_Exp	avg_non_zero	SD	cell_total_count	precent_count	cell_mean_expression	cell_mean_expression_sum	cell_mean_expression_sd
43	4	B_cells	58	149	2.328	2.679	1768	3.281	0.005	9.333	1.457
44	4	CD45	265	585	2.208	2.528	1768	14.989	0.189	335	23
45	4	CD8_T_cells	41	94	2.136	2.446	1768	2.319	0.015	27	5
46	4	Cytotoxic_cells	387	1881	3.329	3.853	1768	21.889	0.072	126.6	12.272
47	4	DC	1	1	1.000	NA	1768	0.057	0	0.333	0.333
48	4	Exhausted_CD8	99	151	1.480	1.657	1768	5.600	0.016	27.75	2.926
49	4	Macrophages	391	769	1.835	2.167	1768	22.115	0.07	123.5	6.973
50	4	Neutrophils	546	1239	1.998	2.304	1768	30.882	0.06	106.286	5.159
51	4	NK_CD56dim_cells	7	19	2.714	2.928	1768	0.396	0.001	2.25	0.901
52	4	NK_cells	9	11	1.000	0.000	1768	0.509	0.002	3.667	1.291
53	4	T_cells	259	719	2.153	2.488	1768	14.649	0.039	69.833	5.398
54	4	Th1_cells	8	8	1.000	0.000	1768	0.452	0.005	8	2.828

	Cluster	Signature	Barcode_count	total_all_gene_Exp	avg_non_zero	SD	cell_total_count	precent_count	cell_mean_expression	cell_mean_expression_sum	cell_mean_expression_sd
55	5	CD45	2	2	1.000	0.000	75	2.667	0.027	2	1.414
56	5	CD8_T_cells	1	7	7.000	NA	75	1.333	0.013	1	1
57	5	Cytotoxic_cells	21	147	3.769	4.837	75	28.000	0.192	14.4	6.81
58	5	Macrophages	34	177	5.206	3.208	75	45.333	0.223	16.75	3.172
59	5	NK_cells	1	1	1.000	NA	75	1.333	0.004	0.333	0.333
60	5	T_cells	6	35	3.182	3.027	75	8.000	0.033	2.5	1.213
61	5	Th1_cells	1	1	1.000	NA	75	1.333	0.013	1	1

	Cluster	Signature	Barcode_count	total_all_gene_Exp	avg_non_zero	SD	cell_total_count	precent_count	cell_mean_expression	cell_mean_expression_sum	cell_mean_expression_sd
62	6	B_cells	2187	21816	4.088	3.624	2282	95.837	0.507	1157.889	29.179
63	6	CD45	539	1249	2.317	2.581	2282	23.620	0.3	684	32.741
64	6	CD8_T_cells	59	149	2.191	2.639	2282	2.585	0.02	44.5	7.194
65	6	Cytotoxic_cells	377	2065	3.542	4.474	2282	16.521	0.063	143.7	18.319
66	6	Exhausted_CD8	59	77	1.305	1.329	2282	2.585	0.007	15.5	2.062
67	6	Macrophages	82	116	1.398	1.592	2282	3.593	0.01	22.75	2.704
68	6	Mast_cells	1	1	1.000	NA	2282	0.044	0	0.25	0.25
69	6	Neutrophils	20	20	1.000	0.000	2282	0.876	0.001	2.857	0.639
70	6	NK_CD56dim_cells	20	20	1.000	0.000	2282	0.876	0.002	5	1.118
71	6	NK_cells	5	5	1.000	0.000	2282	0.219	0.001	1.667	0.745
72	6	T_cells	306	1375	2.847	3.011	2282	13.409	0.051	116.667	8.715
73	6	Th1_cells	16	16	1.000	0.000	2282	0.701	0.007	16	4
74	6	Treg	1	1	1.000	NA	2282	0.044	0	1	1

	Cluster	Signature	Barcode_count	total_all_gene_Exp	avg_non_zero	SD	cell_total_count	precent_count	cell_mean_expression	cell_mean_expression_sum	cell_mean_expression_sd
75	7	B_cells	74	270	2.477	3.066	5900	1.254	0.003	20.111	3.7
76	7	CD45	2104	6099	2.899	2.948	5900	35.661	0.503	2969	73.451
77	7	CD8_T_cells	2505	10733	3.266	3.113	5900	42.458	0.421	2483	58.292
78	7	Cytotoxic_cells	5882	283649	7.919	5.925	5900	99.695	3.563	21021.4	295.397
79	7	DC	1	1	1.000	NA	5900	0.017	0	0.333	0.333
80	7	Exhausted_CD8	996	1769	1.663	1.924	5900	16.881	0.051	299.75	10.359
81	7	Macrophages	92	151	1.641	2.020	5900	1.559	0.004	26.5	3.202
82	7	Neutrophils	12	12	1.000	0.000	5900	0.203	0	1.714	0.495
83	7	NK_CD56dim_cells	414	713	1.647	1.908	5900	7.017	0.021	122	6.461
84	7	NK_cells	1052	2835	2.305	2.589	5900	17.831	0.089	523.333	19.206
85	7	T_cells	3853	33071	4.142	3.510	5900	65.305	0.42	2477.167	47.877
86	7	Th1_cells	848	1558	1.837	2.108	5900	14.373	0.166	978	35.609
87	7	Treg	7	7	1.000	0.000	5900	0.119	0.001	7	2.646

	Cluster	Signature	Barcode_count	total_all_gene_Exp	avg_non_zero	SD	cell_total_count	precent_count	cell_mean_expression	cell_mean_expression_sum	cell_mean_expression_sd
88	8	B_cells	132	635	3.489	3.304	202	65.347	0.162	32.778	3.561
89	8	CD45	16	29	1.812	2.228	202	7.921	0.094	19	5.196
90	8	CD8_T_cells	6	18	3.000	3.098	202	2.970	0.02	4	1.732
91	8	Cytotoxic_cells	183	1727	7.256	4.298	202	90.594	0.521	105.3	10.058
92	8	Exhausted_CD8	3	3	1.000	0.000	202	1.485	0.004	0.75	0.433
93	8	Macrophages	59	170	2.576	2.701	202	29.208	0.105	21.25	3.072
94	8	Neutrophils	8	8	1.000	0.000	202	3.960	0.006	1.143	0.404
95	8	NK_CD56dim_cells	1	1	1.000	NA	202	0.495	0.001	0.25	0.25
96	8	NK_cells	1	1	1.000	NA	202	0.495	0.002	0.333	0.333
97	8	T_cells	35	176	3.592	3.175	202	17.327	0.063	12.667	2.539
98	8	Th1_cells	2	2	1.000	0.000	202	0.990	0.01	2	1.414

	Cluster	Signature	Barcode_count	total_all_gene_Exp	avg_non_zero	SD	cell_total_count	precent_count	cell_mean_expression	cell_mean_expression_sum	cell_mean_expression_sd
99	9	B_cells	1	1	1.0	NA	25	4	0.004	0.111	0.111
100	9	Cytotoxic_cells	4	4	1.0	0.000	25	16	0.016	0.4	0.2
101	9	Macrophages	10	16	1.6	1.897	25	40	0.11	2.75	0.901
102	9	T_cells	2	2	1.0	0.000	25	8	0.013	0.333	0.236

Cluster	Signature	Barcode_count	total_all_gene_Exp	avg_non_zero	SD	cell_total_count	precent_count	cell_mean_expression	cell_mean_expression_sum	cell_mean_expression_sd
10	Macrophages	1	1	1	NA	1	100	0.25	0.25	0.25
10	Mast_cells	1	9	3	3.464	1	100	1	1	1

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for( i in 1:length(mean_score[1,])){
print(visualize_me(mean_score[,i],cell_list[i],analysis_results$tsne[c("TSNE.1","TSNE.2")],title=names(cell_list)[i]))

#print(plot(mean_score[,i],type = "h",xlab="Single Cell",ylab=colnames(mean_score)[i]))
h <-hist(mean_score[,i],plot = FALSE)

h<- plot(h, freq = TRUE, labels =TRUE, ylim=c(0, 1.2*max(h$counts)),main=c(names(cell_list)[i]," Score per Single Cell"),xlab=paste(sep=" ",names(cell_list)[i],"Expression Level"),ylab="Numbers of cells")
#lay_out(list(h, 1, 1),
#       list(vm, 1, 2))
}